Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Obtaining White and pial surface maps for multiple subjects
by Dev vasu 15 Jul '16

15 Jul '16

Dear sir, I would like to know how could i possibly generate white and pial surface data for pool of 50 subjects ( 25 healthy controls and 2 subjects with BLVP) using free surfer. Thanks Vasudev

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Re: [Freesurfer] RB_all_2008-03-26.gca
by Gabor Perlaki 15 Jul '16

15 Jul '16

Dear Bruce, Some subcortical structures seems to be suboptimally segmented in our subjects. By looking at the original MRI intesities and labels of the atlas subjects individually we may suspect that the segmentation of these structures were also suboptimal in the atlas subjects (so the gca atlas is suboptimal), or it is rather related to some demographic/disease related differences between the training data and our subjects, and/or it is a segmentation algorithm related issue. Best Regards, Gabor 2016-07-14 15:30 GMT+02:00 Gabor Perlaki <petzinger.gabor(a)gmail.com>: > Dear all, > > Is it possible somehow to visually inspect the segmentations of the > individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract > the means, priors and labels, but I am rather interested in the original > MRI intensities and labels for the individual subjects. > > Best Regards, > Gabor > > <petzinger.gabor(a)gmail.com> > -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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Freesurfer autorecon2 problem
by Li,Tengfei 15 Jul '16

15 Jul '16

Dear Freesurfers, I am now trying to do recon-all -autorecon1 and recon-all autorecon2 and then do the quality control. When I try " recon-all -autorecon1 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " It works. However, next when I do " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 " or " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " I always get an error. and the error message is " recon-all -s ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 exited with ERRORS at Thu Jul 14 18:19:02 CDT 2016 For more details, see the log file /workspace/tli3/freesurfer_try_onestep_0559_0815/ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582/scripts/recon-all.log " Could someone help me with this? Thx! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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freesurfer autorecon2 problem
by Li,Tengfei 15 Jul '16

15 Jul '16

Dear Freesurfers, I am now trying to do recon-all -autorecon1 and recon-all autorecon2 and then do the quality control. When I try " recon-all -autorecon1 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " It works. However, next when I do " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 " or " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " I always get an error. and the error message is " recon-all -s ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 exited with ERRORS at Thu Jul 14 18:19:02 CDT 2016 For more details, see the log file /workspace/tli3/freesurfer_try_onestep_0559_0815/ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582/scripts/recon-all.log " Error report is attached. Could someone help me with this? Thx! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Research Position
by Mcnorgan, Christopher 14 Jul '16

14 Jul '16

Hi Freesurfers, I wanted to bring to the attention of recent graduates a research assistant position in my lab. Briefly, the position entails the application and transfer of your proficiency with FreeSurfer in the acquisition and analysis of fMRI data collected from healthy adults. More details can be found at the URL below: https://www.ubjobs.buffalo.edu/applicants/jsp/shared/position/JobDetails_cs… Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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question about stats
by Zachariah Holub 14 Jul '16

14 Jul '16

I have run various batches of freesurfer on our MRI scans. Now I want to take many of the stats files from all of our subjects and export them to one giant excel document. I would like to have a separate sheet for each kind of statistic (i.e. Sheet1=LH aparc.2009a; Sheet2=RH aparc.2009a; Sheet3=LH DKT etc...) and then have all of the subjects for that statistic type be included in the appropriate, single sheet. Is there a program that you are aware of that I can use to export the stat files to excel? I would greatly appreciate any insight or help you can offer as it is taking me forever to do this by simply copy and paste. Thank you in advance,Zach

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command line for cp in freeview
by Mihaela Stefan 14 Jul '16

14 Jul '16

Hello Freesurfers, What is the command line to load the control.dat file (control points) in freeview? We tried -cp but it didn't work. Thanks! Mihaela

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mpr2mni305 failed
by Marita Partanen 14 Jul '16

14 Jul '16

Hi I have run recon-all successfully in the past, but now I am getting an error of mpr2mni305 failed, see transforms/talairach_avi.log. I'm running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. This issue appears the same as a recent post http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47393.html but I couldn't see a solution. Any ideas? Here's the full error log: /Users/ophthalmologylab/Studies/Dyslexia_MRI/Intervention/freesurfer/DEGDY001B/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin cfri2163m.bcricwh.lan 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 Fri Jun 17 13:29:22 PDT 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.14, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.91038e-11, -3.72529e-09) j_ras = (-3.72529e-09, -5.82077e-11, -1) k_ras = (7.27596e-12, 1, -5.82077e-11) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 126.275; 0.000 -0.000 1.000 -112.522; -0.000 -1.000 -0.000 132.333; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 17 13:29:25 PDT 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 17 13:29:25 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted _________________________________ Marita Partanen, M.Sc., M.Ed. Ph.D. Candidate in School Psychology The University of British Columbia 2125 Main Mall Vancouver, BC V6T 1Z4 partanen(a)alumni.ubc.ca<mailto:partanen@alumni.ubc.ca>

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Re: [Freesurfer] CVS question
by Michael Zeineh 14 Jul '16

14 Jul '16

> Date: Thu, 14 Jul 2016 10:35:43 -0400 (EDT) > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] CVS question > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607121530370.50358(a)semmelweis.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Michael, > >> I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. >> >> I?ve gotten CVS to work very well registering one subject to another, it really is impressive >> >> However, using the --mni option, it doesn?t work so well, perhaps because the atlas is so averaged together and smoothed out, the images look highly warped. >> >> I know I can pick a subject at random, and register everything to that, but that may induce some biases. The following website suggests I might try simply creating my own atlas (under the answers to Nov 2014 course questions):?https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAn… >> >> Seems like they register 40 subjects with each other for multiple iterations, average the brain together, then run recon-all on that. How does one actually do that, however? i.e. 1st round, register everyone to subject 1 ? then what? Seems like somehow you would want a registration intermediate point somehow? > > Have you tried to use the default cvs atlas? If you do not indicate any > explicit targets that is what will get used. I think that might be a > solution that you are looking for. > > Lilla > > ------------------------------ > Thank you, I happened to try that after I had sent this help request, and yes, it works much, much better. The transformation to MNI space is highly warped, that I realize was the problem. Thank you for your help.

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Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?
by Iglesias, Eugenio 14 Jul '16

14 Jul '16

The MAC version is now fixed as well. It should be available for download in the next couple of days (Zeke can provide a better estimate). Thanks again to all of you for your feedback. /E Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 14 Jul 2016, at 10:05, Fernando Pérez-García <fepegar(a)gmail.com<mailto:fepegar@gmail.com>> wrote: I am using Ubuntu 14.04.4. Please let me know if you need some more info. Cheers, Fernando 2016-07-14 10:59 GMT+02:00 Iglesias, Eugenio <e.iglesias(a)ucl.ac.uk<mailto:e.iglesias@ucl.ac.uk>>: Dear Fernando, Are you using the MAC version? I haven’t finished fixing the bugs in that one yet. If you’re using the Linux version: Zeke, can you please shed some light on what the problem might be? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com<http://www.jeiglesias.com/> http://cmictig.cs.ucl.ac.uk/ On 14 Jul 2016, at 08:57, Fernando Pérez-García <fepegar(a)gmail.com<mailto:fepegar@gmail.com>> wrote: Dear Eugenio, I'm still having this issue, even after downloading the latest development version from the website as you suggested. My steps (yesterday): 1. Download and install FS (dev version) 2. Run recon-all 3. Download and install Matlab runtime 4. Run recon-all with brainstem structures I get the following error: Error:Cannot find CTF archive /usr/local/freesurfer/bin/SegmentSubject.bin.ctf Should I try the same steps again today? Best, Fernando

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